JDOM 2.x exposes a number of 'simple' XMLReaderFactory implementations for use with SAXBuilder, but it is missing one to use a specified/custom JAXP factory. In other words, it has one for http://docs.oracle.com/javase/6/docs/api/javax/xml/parsers/SAXParserFactory.html#newInstance%28%29 but not for: http://docs.oracle.com/javase/6/docs/api/javax/xml/parsers/SAXParserFactory.html#newInstance%28java.lang.String,%20java.lang.ClassLoader%29
A new XMLReaderFactory implementation should be created that uses the missing method (similar to the way we already have XMLReaderSAX2Factory)
See discussion here:
http://markmail.org/message/37rzks5yafjvi4ek